1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
|
/*LICENSE_START*/
/*
* Copyright 1995-2002 Washington University School of Medicine
*
* http://brainmap.wustl.edu
*
* This file is part of CARET.
*
* CARET is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* CARET is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with CARET; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*/
/*LICENSE_END*/
#include "BrainModelSurface.h"
#include "BrainModelSurfaceROINodeSelection.h"
#include "BrainModelSurfaceROITextReport.h"
#include "BrainSet.h"
#include "CommandSurfaceRoiStatisticalReport.h"
#include "FileFilters.h"
#include "LatLonFile.h"
#include "MetricFile.h"
#include "NodeRegionOfInterestFile.h"
#include "PaintFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "SpecFile.h"
#include "SurfaceShapeFile.h"
#include "TextFile.h"
#include "TopologyFile.h"
/**
* constructor.
*/
CommandSurfaceRoiStatisticalReport::CommandSurfaceRoiStatisticalReport()
: CommandBase("-surface-roi-statistical-report",
"SURFACE ROI STATISTICAL REPORT")
{
}
/**
* destructor.
*/
CommandSurfaceRoiStatisticalReport::~CommandSurfaceRoiStatisticalReport()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceRoiStatisticalReport::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Coordinate File Name", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Topology File Name", FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Latitude/Longitude File Name", FileFilters::getLatitudeLongitudeFileFilter());
paramsOut.addFile("Metric File Name", FileFilters::getPaintFileFilter());
paramsOut.addString("Metric Distortion Column Name or Number");
paramsOut.addFile("Paint File Name", FileFilters::getPaintFileFilter());
paramsOut.addFile("Surface Shape File Name", FileFilters::getSurfaceShapeFileFilter());
paramsOut.addFile("Region Of Interest File Name", FileFilters::getRegionOfInterestFileFilter());
paramsOut.addFile("Output Text Report File Name", FileFilters::getTextFileFilter());
paramsOut.addBoolean("Tab Separate Report", false);
}
/**
* get full help information.
*/
QString
CommandSurfaceRoiStatisticalReport::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<coordinate-file-name> \n"
+ indent9 + "<topology-file-name>\n"
+ indent9 + "<latitude-longitude-file-name> \n"
+ indent9 + "<metric-file-name>\n"
+ indent9 + "<metric-distortion-column-name-or-number>\n"
+ indent9 + "<paint-file-name>\n"
+ indent9 + "<surface-shape-file-name>\n"
+ indent9 + "<region-of-interest-file-name> \n"
+ indent9 + "<output-text-report-file-name> \n"
+ indent9 + "<tab-separate-report-flag>\n"
+ indent9 + "\n"
+ indent9 + "Generate a staistical report. If any of the data files \n"
+ indent9 + "(lat/long, paint, metric, or shape) are not available, \n"
+ indent9 + "specify its name two consecutive double quotes (\"\"). \n"
+ indent9 + "\n"
+ indent9 + "If there is not a metric distortion column, specify its\n"
+ indent9 + "value with two consecutive double quotes (\"\").\n"
+ indent9 + "\n"
+ indent9 + "\"tab-separate-report-flag\" value is either \"true\" or \n"
+ indent9 + "\"false\".\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceRoiStatisticalReport::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get the parameters
//
const QString coordinateFileName =
parameters->getNextParameterAsString("Coordinate File Name");
const QString topoFileName =
parameters->getNextParameterAsString("Topology File Name");
const QString latLonFileName =
parameters->getNextParameterAsString("Lat/Lon File Name");
const QString metricFileName =
parameters->getNextParameterAsString("Metric File Name");
const QString metricColumnNameOrNumber =
parameters->getNextParameterAsString("Metric Distortion Column Name or Number");
const QString paintFileName =
parameters->getNextParameterAsString("Paint File Name");
const QString surfaceShapeFileName =
parameters->getNextParameterAsString("Surface Shape File Name");
const QString roiFileName =
parameters->getNextParameterAsString("Region of Interest File Name");
const QString textReportFileName =
parameters->getNextParameterAsString("Text Report File Name");
const bool tabSeparateReportFlag =
parameters->getNextParameterAsBoolean("Tab Separate Report Flag");
//
// Read the spec file into a brain set
//
SpecFile specFile;
specFile.addToSpecFile(SpecFile::getFiducialCoordFileTag(),
coordinateFileName,
"",
false);
specFile.addToSpecFile(SpecFile::getClosedTopoFileTag(),
topoFileName,
"",
false);
specFile.addToSpecFile(SpecFile::getLatLonFileTag(),
latLonFileName,
"",
false);
specFile.addToSpecFile(SpecFile::getMetricFileTag(),
metricFileName,
"",
false);
specFile.addToSpecFile(SpecFile::getPaintFileTag(),
paintFileName,
"",
false);
specFile.addToSpecFile(SpecFile::getSurfaceShapeFileTag(),
surfaceShapeFileName,
"",
false);
//
// Read the spec file into a brain set
//
QString errorMessage;
BrainSet brainSet(true);
brainSet.setIgnoreTopologyFileInCoordinateFileHeaderFlag(true);
if (brainSet.readSpecFile(specFile, "", errorMessage)) {
throw CommandException("Reading spec file: " +
errorMessage);
}
//
// Find the surface
//
BrainModelSurface* bms = brainSet.getBrainModelSurface(0);
if (bms == NULL) {
throw CommandException("Unable to find surface after reading files.");
}
//
// Read the roi
//
BrainModelSurfaceROINodeSelection roi(&brainSet);
NodeRegionOfInterestFile roiFile;
roiFile.readFile(roiFileName);
roi.getRegionOfInterestFromFile(roiFile);
//
// Find the metric distortion column number and set selected columns
//
MetricFile* metricFile = brainSet.getMetricFile();
int metricDistortionColumnNumber = -1;
if ((metricFile->empty() == false) &&
(metricColumnNameOrNumber.isEmpty() == false)) {
metricDistortionColumnNumber = metricFile->getColumnFromNameOrNumber(metricColumnNameOrNumber, false);
}
std::vector<bool> metricSelections(metricFile->getNumberOfColumns(), true);
//
// Paint selections
//
PaintFile* paintFile = brainSet.getPaintFile();
std::vector<bool> paintSelections(paintFile->getNumberOfColumns(), true);
//
// Shape selections
//
SurfaceShapeFile* shapeFile = brainSet.getSurfaceShapeFile();
std::vector<bool> shapeSelections(shapeFile->getNumberOfColumns(), true);
//
// Verify surface has nodes
//
const int numNodes = brainSet.getNumberOfNodes();
if (numNodes <= 0) {
throw CommandException("The surfaces contain no nodes.");
}
//
// Run the statistical report
//
BrainModelSurfaceROITextReport bmsri(&brainSet,
bms,
&roi,
metricFile,
metricSelections,
shapeFile,
shapeSelections,
paintFile,
paintSelections,
brainSet.getLatLonFile(),
0, // lat/lon file column
"",
metricFile,
metricDistortionColumnNumber,
tabSeparateReportFlag);
try {
bmsri.execute();
}
catch (BrainModelAlgorithmException& e) {
throw CommandException(e.whatQString());
return;
}
//
// File for text report
//
TextFile textReportFile;
textReportFile.setText(bmsri.getReportText());
//
// Write the text file
//
textReportFile.writeFile(textReportFileName);
}
|
